GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas fluorescens FW300-N2C3

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AO356_24390 AO356_24390 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_24390
          Length = 869

 Score = 1377 bits (3563), Expect = 0.0
 Identities = 667/859 (77%), Positives = 761/859 (88%), Gaps = 3/859 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           +LE YRKH+ ERAA GI P+PL+A Q A L+ELLKNPPAGEE FL+DL+TNRVPPGVDEA
Sbjct: 1   VLEAYRKHIEERAALGIVPQPLNAEQTAGLIELLKNPPAGEEAFLVDLITNRVPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL+A+AKG+A+SPLL  ++A+ELLGTMQGGYNI  L++ LDDA+LAP+AAK L 
Sbjct: 61  AYVKAGFLSALAKGQAQSPLLDKKRAVELLGTMQGGYNIVTLVELLDDAELAPVAAKELK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD F+DV EKAK GN +AK V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNVHAKAVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLK AR+GI PD+ G  GP+KQIE ++ +GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDEQGKTGPMKQIEEMRGQGFPIAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDD+P VPNKR GG C G KIAPIF+NTMEDAGALPIE DVSN
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPFVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSN 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           ++MGDVID+YP+ G+V  H T E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR  
Sbjct: 301 MHMGDVIDLYPHAGKVCKHGTDEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGLP  D+F++ +  AES +GF+LAQKMVG+ACG+   +G+RPG YCEPKMT+VGSQDTT
Sbjct: 361 LGLPAFDLFKKPEAPAESTKGFTLAQKMVGKACGLAEGQGVRPGTYCEPKMTTVGSQDTT 420

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDG 480

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           +IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFK
Sbjct: 481 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           GKM+PGITLRDLVHAIP +AI+ GLLTVEKKGKKN FSGRILEIEGL  L +EQAFEL+D
Sbjct: 541 GKMKPGITLRDLVHAIPYFAIQNGLLTVEKKGKKNAFSGRILEIEGLEGLTLEQAFELSD 600

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           ASAERSAAGCTIKL+KE I EYL SNI LL+WMI EGYGD RTLERR Q ME W+ANP+L
Sbjct: 601 ASAERSAAGCTIKLSKESITEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWVANPQL 660

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           +EADADAEYA VI+IDLADI EP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHF
Sbjct: 661 MEADADAEYAEVIEIDLADISEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHF 720

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAAGKLL+  KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLEQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           RV   +TVVSTSTRNFPNRLG GANV+LASAELA+VA+++G+LPT EEY  Y  ++D  A
Sbjct: 781 RVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMEYAGKIDSMA 840

Query: 838 VDTYRYLNFNQLSQYTEKA 856
            D YRYL+F+Q++++ E A
Sbjct: 841 ADVYRYLSFDQIAEFREAA 859


Lambda     K      H
   0.317    0.136    0.400 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2150
Number of extensions: 76
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 865
Length of database: 869
Length adjustment: 42
Effective length of query: 823
Effective length of database: 827
Effective search space:   680621
Effective search space used:   680621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

Align candidate AO356_24390 AO356_24390 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (EC 4.2.1.3))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00117.hmm
# target sequence database:        /tmp/gapView.11002.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00117  [M=844]
Accession:   TIGR00117
Description: acnB: aconitate hydratase 2
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
          0 1527.1   0.0          0 1526.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390  AO356_24390 bifunctional aconita


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390  AO356_24390 bifunctional aconitate hydratase 2/2-methylisocitrate deh
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1526.9   0.0         0         0       1     844 []       1     857 [.       1     857 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1526.9 bits;  conditional E-value: 0
                                       TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayv 63 
                                                     +le+yrkh+ eraa+gi p+plna+q+a l+ellkn+p++ee+fl++l+++rvppgvdeaayv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390   1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLIELLKNPPAGEEAFLVDLITNRVPPGVDEAAYV 63 
                                                     69************************************************************* PP

                                       TIGR00117  64 kagflaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktll 126
                                                     kagfl+a+akg+++spl+  ++avellgtm+ggyn+ +l+e+l+  d+++a++aak l++tll
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390  64 KAGFLSALAKGQAQSPLLDKKRAVELLGTMQGGYNIVTLVELLD--DAELAPVAAKELKHTLL 124
                                                     ********************************************..***************** PP

                                       TIGR00117 127 vfdafddveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapd 188
                                                     +fdaf+dv+e++k  n +ak vl+swa++ewf n++ la+ki+  vfkv+getntddlspapd
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 125 MFDAFHDVAEKAKNgNVHAKAVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTDDLSPAPD 187
                                                     ************998************************************************ PP

                                       TIGR00117 189 aftrpdiplhalamlknkieeieq..........rikalkqkgvpvayvgdvvgtgssrksat 241
                                                     a++rpdiplhalamlk ++++i +          +i++++ +g+p+ayvgdvvgtgssrksat
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 188 AWSRPDIPLHALAMLKMARDGIVPdeqgktgpmkQIEEMRGQGFPIAYVGDVVGTGSSRKSAT 250
                                                     *********************999999************************************ PP

                                       TIGR00117 242 nsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypyk 304
                                                     nsvlwf+g+d+pfvpnkragg+++g kiapif+nt+ed+galpie dv+++++gdvi++yp+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 251 NSVLWFFGDDVPFVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSNMHMGDVIDLYPHA 313
                                                     *************************************************************** PP

                                       TIGR00117 305 geitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapa 366
                                                     g++ ++ t ev++tf++k+ +lldevraggripliigrglt+kar  lgl+  ++fkk++apa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 314 GKVCKHGTdEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAELGLPAFDLFKKPEAPA 376
                                                     ******9999***************************************************** PP

                                       TIGR00117 367 esakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdad 426
                                                     es+kgftlaqk+vgkacg+   +g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf+ad
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 377 ESTKGFTLAQKMVGKACGLaegQGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSAD 439
                                                     ******************86668**************************************** PP

                                       TIGR00117 427 lvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdsh 489
                                                     lv+qsfchtaaypkp+dv th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdsh
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 440 LVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSH 502
                                                     *************************************************************** PP

                                       TIGR00117 490 trfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkgl 552
                                                     trfp+gisfpagsglvafaaatgvmpldmpes+lvrfkg+++pgitlrdlv+aipy+ai++gl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 503 TRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGKMKPGITLRDLVHAIPYFAIQNGL 565
                                                     *************************************************************** PP

                                       TIGR00117 553 ltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksniv 615
                                                     ltvekkgk+n f+grileiegl  l +eqafel+dasaersaagctikl+ke++ eyl+sni 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 566 LTVEKKGKKNAFSGRILEIEGLEGLTLEQAFELSDASAERSAAGCTIKLSKESITEYLQSNIT 628
                                                     *************************************************************** PP

                                       TIGR00117 616 llkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndp 678
                                                     ll++mi egy+d+rtl+rr +ame+w+anp+l+eadadaeya+vieidla+i ep+l+apndp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 629 LLRWMIGEGYGDARTLERRAQAMEAWVANPQLMEADADAEYAEVIEIDLADISEPVLCAPNDP 691
                                                     *************************************************************** PP

                                       TIGR00117 679 ddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmdeqqliee 740
                                                     dd++lls vag++idevfigscmtnighfraagk+le+ k ++++rlw+ ppt+md++ql+ee
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 692 DDARLLSSVAGEKIDEVFIGSCMTNIGHFRAAGKLLEQVKgQLPTRLWLSPPTKMDAHQLTEE 754
                                                     *************************************9988********************** PP

                                       TIGR00117 741 gyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaava 803
                                                     gyy+i+g+agar+e+pgcslcmgnqarve ++tv+ststrnf+nrlg ga+vyl+saela+va
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 755 GYYGIYGKAGARMEMPGCSLCMGNQARVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVA 817
                                                     *************************************************************** PP

                                       TIGR00117 804 allgkiptkeeylalvsekvesakdklyrylnfnelenfee 844
                                                     ++lg++pt+eey+++  + +  a d +yryl f+++ +f+e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 818 SILGRLPTVEEYMEYAGKIDSMAAD-VYRYLSFDQIAEFRE 857
                                                     ***************8877766666.************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (869 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 12.94
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory